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Makefile
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Makefile
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ENV=variants
.PHONY dry-test:
dry-test: tests/input.tsv
mamba run -n $(ENV) snakemake --cores all -np --configfile tests/config.yaml
.PHONY test:
test: tests/input.tsv
rm -rf tests/results
mamba run -n $(ENV) snakemake --use-conda --cores all --configfile tests/config.yaml
diff -s tests/results/sampleA.varscan.tsv tests/results/sampleB.varscan.tsv
tests/input.tsv:
mamba run -n $(ENV) scripts/generate_input.py -o tests/ -m1 _R1 -m2 _R2 tests/data/
.PHONY clean:
clean:
rm -rf tests/results/
rm -f tests/input.tsv
rm -rf .snakemake/
.PHONY style:
style:
mamba run -n $(ENV) snakefmt . # buggy {{name}} -> {name}
sed -i 's/{name}/{{name}}/' workflow/Snakefile # hack
mamba run -n $(ENV) black .
.PHONY env:
env:
mamba env create
.PHONY rm-env:
rm-env:
mamba env remove --name $(ENV)